Prospects & Overviews Review essays The phage-host arms race: Shaping the evolution of microbes Adi Stern and Rotem Sorekà Bacteria, the most abundant organisms on the planet, Introduction are outnumbered by a factor of 10 to 1 by phages that Phage-host relationships have been studied intensively since infect them. Faced with the rapid evolution and turnover the early days of molecular biology. In the late 1970s, while of phage particles, bacteria have evolved various mech- viruses were found to be ubiquitous, it was assumed that they anisms to evade phage infection and killing, leading to were present in relatively low numbers and that their effect on an evolutionary arms race. The extensive co-evolution of microbial communities was low [1]. With the increasing avail- both phage and host has resulted in considerable diver- ability of new molecular techniques that allow studies of microbial communities without the need to culture them sity on the part of both bacterial and phage defensive [2], it is now realized that viruses greatly outnumber bacteria and offensive strategies. Here, we discuss the unique in the ocean and other environments, with viral numbers and common features of phage resistance mechanisms (107–108/mL) often 10-fold larger than bacterial cell counts and their role in global biodiversity. The commonalities (106/mL) [3–5]. Thus, bacteria are confronted with a constant between defense mechanisms suggest avenues for the threat of phage predation. discovery of novel forms of these mechanisms based on The Red Queen hypothesis (Box 1) posits that competitive environmental interactions, such as those displayed by hosts their evolutionary traits. and parasites, will lead to continuous variation and selection towards adaptation of the host, and counter-adaptations on Keywords: the side of the parasite. Arguably, nowhere is this evolutionary .arms race; bacteria; evolution; phage; resistance trend so pronounced as in phage-microbe interactions. This is due to the extremely rapid evolution and turnover of phage particles [6], causing acute pressure on microbial communities to evade infection and killing by phages. In fact, the arms race between phages and bacteria is predicted to have had an impact on global nutrient cycling [7], on global climate [6, 7], on the evolution of the biosphere [8], and also on the evolution of virulence in human pathogens [9]. This review focuses on the evolution of three of the most well-studied microbial defense mechanisms against phages: the restriction-modification (RM) system, the recently discov- ered ‘‘clustered regularly interspersed palindromic repeats’’ (CRISPR) loci together with CRISPR-associated (cas) genes, and the abortive infection (Abi) system (summarized in DOI 10.1002/bies.201000071 Table 1). We first describe these defense systems, and the counter-adaptations that evolved in the phage to allow escape Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel from bacterial defense. Next, we discuss features that are common to many microbial defense systems, such as rapid *Corresponding author: Rotem Sorek evolution, tendency for lateral gene transfer (LGT), and the E-mail: [email protected] selfish nature of these systems. We elaborate on defense Abbreviations: systems that have gained new functions in the host genome. Abi, abortive infection; Cas, CRISPR-associated sequence; CRISPR, Finally, the exciting hypothesis that many other prokaryotic clustered regularly interspersed palindromic repeats; crRNA, CRISPR RNA; LGT, lateral gene transfer; MTase, methyltransferase; REase, restriction defense systems are still to be discovered is discussed. Our endonuclease; RM, restriction modification; TA, toxin-antitoxin. review mainly focuses on the evolutionary angle of the phage- Bioessays 00: 000–000,ß 2010 WILEY Periodicals, Inc. www.bioessays-journal.com 1 A. Stern and R. Sorek Prospects & Overviews .... material and another that protects host genetic material from Box 1 restriction (Fig. 1A). Both activities are mediated by recog- nition of a specific DNA sequence, on average 4–8 bp long. The Red Queen hypothesis Protection is normally conferred by modification (usually methylation) of specific bases in this recognition sequence The Red Queen hypothesis was originally proposed by in the host genome. Accordingly, all non-methylated DNA Van Valen [10], and is also termed the evolutionary arms recognition sequences are recognized as foreign and are race hypothesis. As the Red Queen tells Alice in Lewis cleaved. Genetically, the minimal composition of RM systems Carroll’s Through the Looking-Glass: ‘‘Now, here, you consists of a methyltransferase (MTase) gene that performs the see, it takes all the running you can do, to keep in the defense activity and a restriction endonuclease (REase) gene same place. If you want to get somewhere else, you must that performs the foreign restriction activity. Since the REases run at least twice as fast as that!’’ The original theory undergo rapid evolution, it is often the presence of an MTase proposed that in tight co-evolutionary interactions, such that serves as the basis for identification of RM systems in Review essays as those in a prey-predator relationship, changes (e.g., newly sequenced genomes [14]. running faster) on the one side may lead to near extinc- Phages have evolved to evade the ubiquitous RM systems tion of the other side. The only way the second side can in a variety of ways (Fig. 1B). Some phages have acquired an maintain its fitness is by counter-adaptation (running MTase, or stimulate the host MTase so that it confers protec- even faster). This will lead to an uneasy balance between tion to the phage genome [15]. Other phages code for proteins prey and predator, where species have to constantly that target and shut down the REase. One interesting example evolve to stay at the same fitness level. The metaphor is the Ocr protein of phage T7, which blocks the active site of of an evolutionary arms race has been found to be some REases by mimicking 24 bp of bent B-form DNA [16]. relevant for many biological processes, but nowhere is Alternatively, some phages incorporate unusual bases in their this metaphor as apt as in host-parasite relationships. genomes, thus throwing off the REase. For example, some Bacillus subtilis phages replace thymine with 5-hydroxyme- thyluracil [15]. These phages code a protein that then further inhibits the host protein uracil-DNA glycosylase from cleaving host arms race; for deeper mechanistic descriptions of phage uracil bases from the phage DNA [17, 18]. Interestingly, this resistance systems we refer the readers to an excellent recent inhibitory protein is also a DNA mimic (reviewed in ref. 19). review [11]. In addition, the discussion here is restricted to The T-even phages T2, T4, and T6 also contain unusual bases active defense mechanisms; passive host adaptations, such as in their genomes and may further post-synthetically glycosy- mutations at the phage receptors, are not discussed. late their DNA to avoid REase restriction [15]. Yet another evasion mechanism that has been reported is alteration of the restriction recognition sites. For example, some phages Restriction-modification systems: employ ‘‘palindrome avoidance’’: since Type II REases often Degradation of foreign DNA recognize symmetrical (palindromic) sequences, some phages tend to avoid containing such sites in their genome [20]. Arguably, the most well-studied phage defense mechanism is The well-studied model organisms Escherichia coli and T4 the RM system [12], which is present in over 90% of sequenced phage display a fascinating example of a co-evolutionary arms bacterial and archaeal genomes [13]. This system is composed race [11]. The battle purportedly begins with the T4 phage genome, of two activities: one that restricts incoming foreign genetic which contains the modified base hydroxymethylcytosine instead Table 1. A summary of the major defense mechanisms described in this article Name Mechanism Phylogenetic breadth Restriction-modification The restriction enzyme cleaves specific patterns Appear in 90% of all sequenced in the incoming foreign DNA, while the modification prokaryotic genomes [13] enzyme protects host DNA from cleavage by unique biochemical modification CRISPR/Cas Fragments of phage DNA are integrated into Appear in 40% and 90% of all CRISPR loci, which are then transcribed and sequenced bacterial and archaeal processed into short non-coding RNAs. These genomes, respectively [27]. The RNAs, along with the associated Cas proteins, distribution of CRISPR/Cas-bearing guide the way to interfere with the phage nucleic species across the phylogenetic tree acids, in an as-yet-unknown mechanism of life is highly patchy [38, 59] Abortive infection Premature cellular death occurs upon phage entry, Currently known Abi systems display blocking the expansion of the phage to neighboring a sporadic phylogenetic distribution in cells. Notably, Abi systems include a large collection Gamma-proteobacteria and in Firmicutes [44], of mechanisms with little or no known evolutionary yet recent reports suggest that some relationship, apart from a very similar phenotype systems may have an even broader phylogenetic range [54, 111] 2 Bioessays 00: 000–000,ß 2010 WILEY Periodicals, Inc. ....Prospects & Overviews A. Stern and R. Sorek CRISPR/Cas: Acquired adaptive immunity The existence of a unique nucleotide arrangement in E. coli, Review essays comprised of a cluster of direct repeats interspersed with variable sequences (termed spacers; both around 30 bp long), was first described in 1987 [25]. These clusters, together with associated cas genes (Fig. 2A), were later found to exist in 40% of sequenced bacterial genomes and 90% of archaeal genomes [26–28]. The first inkling that this system comprises a phage-defense mechanism arose when spacer sequences were found to be highly similar to DNA from foreign origin, i.e. from phage, plasmid or transposon DNA [29–31]. In 2007, exper- imental evidence was presented that this system indeed con- fers resistance to phage infection [32]. This led to the striking insight that similar to vertebrates, prokaryotes possess acquired (and inherited) immunity [27, 33–35].